Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaaaaaaaaaatcatcactcctttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG

Basic information

species Vitis vinifera
transcript Vv01s0026g00310.t01
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G030144_T01 (Zea mays), 3'ss of exon 2
caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaaaaaaaaaatcatcactcctttgcaggaaccttaactta---tatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
                     ||    ||  | |    ||  |   |    |       |   | ||   |  |||          | |||||   |    |||||||| || ||    ||||||| |||||| || ||||| || ||||| || || ||||| ||||| || |||||||| ||||||||||| |||||||||
---------------------gtatccaccctgtctgcacttaacagttgtgtttgttgattgttatgcgttgtttctgattgtaattacttaacgtgggcagAGATCTTAACCACTCAAACCAGTTCATTGTTGGTCTTGCACTCTGTGCCCTTGGCAATATATGTTCTGCTGAAATGGCGCGTGATCTTGCTCCTGAAGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaaaaa-aaaaatcatcactcctttgcag--gaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
                                                          | |    |    |||     |||  |  ||| | |||||  |    ||| ||   || ||| || |  | |   ||  ||  || |||||||| |     |||||||| ||||| |  || ||||| || ||||||||||||||||||||| | ||||| ||||||||||||||||||||||||||||||||||| || || 
gtatccagtttttagtcaaagttctgtttattttttttatttatattccctgatttttacattgcattttacaaatgtgttattttgatctacttactgaaataaaatgagggaacaaatattaataatgggttatagcagagccttaactgaatcacagAGATCTTAATCACACAAATCAGTATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAACATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCAGAGGTT

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------caaaaaaaaaaaaacattatcgttggtacgatattct---tacaaagtcgaaaagaaaaaaaaaaatcatcactcct---ttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
                                                     | |    |    |||     |||  |  ||| ||||   |||  |  | ||| ||| ||||||||  || | |  |   ||    || |||||||| |     |||||||| ||||| |  || ||||| || ||||||||||||||||||||| | ||||| |||||||||||||||||||| |||||||||||||| || || 
gtatccagtttttagtcaaagttctgtttatctttttatattgcctgatttttacatttcactttacaaatgtgttattttgatcttctacttactgaaacaaaatgaagaaaaaaaaatattaataatgggttagtagagccttaactgaatcacagAGATCTTAATCACACAAATCAGTATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAACATTTGTTCAGCAGAAATGGCCCGTGATCTTGCACCAGAGGTT

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 2
--------------------------caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaaaaaaaaaatcatcactcctttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
                                        | |||   ||   |    ||| |   ||  |   |  ||   |  || |       |   ||  |  ||||||| || |     |||||||| ||||| |  || || || || ||||||||||||||||||||| | |||||||||| |||||| ||||||||||||||||||||||| || || 
gtatccaaattcatgtcaatgtttcatttgtttttgtgttccttaatttttagattccattttacaaatatgctagggagctagcaataatggtgatgggttataaaaaccttagctaagtcacagAGATCTTAATCACACAAATCAATATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAATATTTCTTCAGCCGAAATGGCTCGTGATCTTGCACCAGAGGTT

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------caaaaaaaaaaaaacattat-cgttggtacgatattcttacaaagtcgaaaagaaaaaaaaaaatcatcactcc--tttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
                 ||      |   | || |  | |||   | ||        |  |  |       | ||| |  | | | |   |||   ||||||| |||||  | ||||||||| ||||| |  ||||||||||||||||| |||||||| |||||| | ||||||||||||||||||||||||||||||||||| || |||||||| 
gtatcctttatggtgttaatttttgattttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S211_68V6.1 (Physcomitrella patens), 3'ss of exon 2
caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaaa--aaaaaaatcatcactcctttgcaggaacct--taacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
  |               ||| |   | | || |  ||    | | ||   | | |  | |    || | ||   |   |  | |  |  |   || | |  || ||  | | ||| |  ||||||| |||||||||| | ||||||||||| || || || |||||| | || ||||||||  | |||||||| |||||||||
--agtgctctggggttacatc-tcaattcaat-tcattgttcattagattggcatatcagacgcgtctttaccagtacacgtgtatttgttgttttttctgcagTGACTTGAGTCACACAAACCAGTTCATTGTGGGATTGGCTCTTTGTGCACTTGGCAACATTTGTACTGCTGAAATGGCAAGGGATCTTGCTCCTGAAGTG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S91_146V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaa---aaaaaaaatcatcactcctttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
             ||||  |    ||| |  |     || |  |||       | | ||  |  |  |   |    |     ||  |  | |   || | ||||||| | |   || || ||  || |||  || ||  |  | |  ||||| ||||||||||||||||| ||||| ||  ||||||| ||||||||||||               
gggcatttagattcaaaccagtccaaataagaggtcaggcataataggggaggacattcacatggccacttatcgcacgaagtctattttcttttgggagCTTAACTCA-AGGAAGTGACCTACATGATACAAATCAACATGTCGCTGGACTGGCTCTTTGTGCTCTGGGCAATATCTGCACAGCAGATATGGCTCGTGAT---------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|161718068|gb|FC068577.1|FC068577
EST:     CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACA                         AGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT
genomic: CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaatt ... ttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT
EST: gi|110720727|gb|EE096900.1|EE096900
EST:     CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACA                         AGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT
genomic: CTTGATGAAAGGCAAGAAGTTCTTATGTTGGTTACAAACTCATTAAAACAgtatccaatt ... ttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaaaagaaaaaaaaaaatcatcactcctttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG
                                    aaccttaac  putative branch site 
     agaaaaaaaaaaatca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaaaaaaaaaaacattatcgttggtacgatattcttacaaagtcgaaaagaaaaaaaaaaatcatcactcctttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
caaaaaa
-aaaaaaa
- - - - - - - - - - - - - - - - - - - -caaagtc
- - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaac